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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaacacaaactaaacctaatgtagattgcaatcaaattgaaaacaaaacaattgcttcggattaataaattgcgtgtttatcctcagGTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTGGCATATGCTGCACATAAAGCTGCATCTCCAATTAGGTTTCCACCCACAG

Basic information

species Glycine max
transcript GLYMA11G18410.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G18410.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G27290.1 (Arabidopsis thaliana), 3'ss of exon 2
-gtgcaacacaaactaaac--ctaatgtagattgcaatcaaattgaaaacaaaacaattgcttcggattaataaattgcgtgtttatcctcagGTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTGGCATATGCTGCACATAAAGCTGCATCTCCAATTAGGTTTCCACCCACAG
  | | ||    |||        |   ||  ||    |    ||||          | |    | ||||   |  ||  |||||||     ||||||| || || ||  ||| ||| ||||||||||| ||  ||||||| ||||| || || || ||||||||||||||||| || |||||||| || ||||
gttactactttcacttcttgatcatactaagtttatgttttcttgatcttgggttgagtaaagctgattttgatgttttgtgttta-----agGTTGGGATTTCGACGAATGAGACAGGAGAGAAAGTAGGAGCCTTTGCTTTGGCTTACGCAGCGCATAAAGCTGCATCTCCGATAAGGTTTCCGCCTACAG

upper sequence: GLYMA11G18410.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0080g01100.t01 (Vitis vinifera), 3'ss of exon 2
gtgcaacacaaactaaacctaatgtagattgcaatcaaattgaaaacaaaacaatt--gcttcggattaataaa-ttgcgtgtttatcctcagGTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTGGCATATGCTGCACATAAAGCTGCATCTCCAATTAGGTTTCCACCCACAG
             ||     | || | | |  || |    |  | ||||||  | |  | || |||  |||    |||  || | |    ||||| ||||| ||    ||||||||||| |||||||| || || |||||||||||||||||||||||||| ||||||||||| || ||||| |||||||| |
------------gtacttgaattgcaaactttaagcttcctccatacaaaaataataggtttgggagcaatggtcttgattgctgagttgcagGTGGGAATATCTGTGGATGCGACTGGGGAGAAAGTAGGGACGTTTGCATTGGCATATGCTGCACATAAGGCTGCATCTCCTATAAGGTTCCCACCCACCG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|192320459|gb|FK012317.1|FK012317
EST:     GTTATGCATTAATTAGCGCTGGAATTGATGTACAATCTTTACTGCAGAAG                         GTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTG
genomic: GTTATGCATTAATTAGCGCTGGAATTGATGTACAATCTTTACTGCAGAAGgtgcaacaca ... ttatcctcagGTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTG
EST: gi|209727232|gb|BW655243.1|BW655243
EST:     GTTATGCATTAATTAGCGCTGGAATTGATGTACAATCTTTACTGCAGAAG                         GTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTG
genomic: GTTATGCATTAATTAGCGCTGGAATTGATGTACAATCTTTACTGCAGAAGgtgcaacaca ... ttatcctcagGTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTG
EST: gi|209725059|gb|BW659781.1|BW659781
EST:     GTTATGCATTAATTAGCGCTGGAATTGATGTACAATCTTTACTGCAGAAG                         GTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTG
genomic: GTTATGCATTAATTAGCGCTGGAATTGATGTACAATCTTTACTGCAGAAGgtgcaacaca ... ttatcctcagGTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTG
EST: gi|209725060|gb|BW659782.1|BW659782
EST:     GTTATGCATTAATTAGCGCTGGAATTGATGTACAATCTTTACTGCAGAAG                         GTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTG
genomic: GTTATGCATTAATTAGCGCTGGAATTGATGTACAATCTTTACTGCAGAAGgtgcaacaca ... ttatcctcagGTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTG
EST: gi|192320458|gb|FK012316.1|FK012316
EST:     GTTATGCATTAATTAGCGCTGGAATTGATGTACAATCTTTACTGCAGAAG                         GTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTG
genomic: GTTATGCATTAATTAGCGCTGGAATTGATGTACAATCTTTACTGCAGAAGgtgcaacaca ... ttatcctcagGTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaattgaaaacaaaacaattgcttcggattaataaattgcgtgtttatcctcagGTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTGGCATATGCTGCACATAAAGCTGCATCTCCAATTAGGTTTCCACCCACAG
                           gattaat  putative branch site (score: 3)
                                            tttatcctc  putative PPT
       aaaacaaaacaatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcaacacaaactaaacctaatgtagattgcaatcaaattgaaaacaaaacaattgcttcggattaataaattgcgtgtttatcctcagGTTGGAATCTCAACTGATGCGACTGGAGAGAAAGTTGGTACCTTTGCATTGGCATATGCTGCACATAAAGCTGCATCTCCAATTAGGTTTCCACCCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC